ere have been so many articles on genomics-related topics in recent months that this issue of the Digest would need to be very long indeed to present even the tightest summary. However, the articles seemed to fit more or less nicely into one of three categories: The accelerating development of genomics technologies and initiatives, the impact this has on genomics understanding, and the impact that has in terms of genetic therapies for disease. Therefore, we have divided this issue into three parts, to be published serially. This is part 2…

The Acceleration of Genomics Understanding

Understanding the Genetics of Disease

Our increasing ability to detect changes in DNA that lead to disease heralds a paradigm shift in diagnostics and, therefore, in clinical practice. The genome scan is fast becoming diagnostically more informative than patients’ symptoms and conventional lab tests, which can only identify much larger structural changes. For example, it was recently discovered that the deletion of a set of seven genes can trigger a wide variety of cognitive problems, including autism, mental retardation, and developmental delay. Two other studies have linked a deletion in the same region of the genome to increased risk of schizophrenia. A third study has identified structural variation in a different part of the genome that appears to be responsible for about 1 percent of autism cases—“the largest genetic culprit found to date” as an MIT Technology Review writer put it.

One geneticist told the Review he expected “that within the next year or so, [genetic scanning for the seven deletions] will become the primary genetic test in the pediatric setting for children with any unexpected developmental abnormality.” The test can also be used on parents of afflicted children, who could be mildly affected by the same condition. It can also be used in counseling such parents who wish to have another child.

Some US researchers are already seeking patents to cover a blood test that looks for another gene combination; this time, one that identifies prostate cancer. It turns out that a combination of five genetic markers, used together with a family history of the disease, constitute a highly predictive biomarker for prostate cancer, one much better than the PSA test. The proposed genetic blood test would enable men at high risk to be monitored and perhaps offered preventive treatments.

UK researchers have also discovered seven genes associated with prostate cancer. A clinical trial due to begin in late 2008 will screen for the risk genes in men with a family history of the cancer. The British researchers are more cautious in predicting a genetic profiling test for prostate cancer risk, estimating “within three to four years.”

The complex genetics of another childhood disease, Down’s syndrome, are also being unraveled. An international study using mice has revealed the chain of genetic changes caused by the presence of an extra copy of chromosome 21 in a developing embryo, which lead to Down’s syndrome. The condition is one of a group called aneuploidies, defined by an abnormal loss or gain of genetic material, which are a prime cause of infant death. This study’s findings could one day lead to regenerative therapies to alleviate the effects not only of Down’s syndrome but also of developmental delay, mental retardation, aging, and Alzheimer’s disease.

Another recent genetics breakthrough was the discovery of an anti-oxidant pathway that makes acute myeloid leukemia (AML) cells resistant to treatment. When the pathway is inhibited, the cells lose their resistance and become responsive to drugs. This discovery could lead to new drugs for patients not just with AML but also with other forms of leukemia.

And yet another recent hit from genetic research on cancer, this time involving the brain, is the discovery that there are in fact three subgroups of glioblastoma tumors, and that some are deadlier than others. The difference depends on the degree of methylation, or chemical modifications to the patient’s DNA [a key component of the splicing mentioned later in this issue.] Methylation status may thus serve as “a robust, and previously unexplored, source of biomarkers for this disease,” the study’s lead author told the American Association for Cancer Research.

However, current techniques are either not sensitive enough to detect small amounts of methylation or are too expensive. Johns Hopkins researchers have overcome these problems with a method of methylation screening that “provides an easy, cost-effective and valuable tool for the early diagnosis of cancer, monitoring tumor behavior and measuring the response of tumors to targeted cancer therapies,” a researcher told the AACR. The provisionally patented system allows for minimal handling and simultaneous processing and analysis of multiple samples. It has accurately detected methylation for a gene that promotes programmed cell death, in low concentrations of DNA from human sputum. It was also used to quantify the amount of methylation reversal in bone marrow fluid samples taken from patients with myelodysplastic syndrome (a disorder in which bone marrow cells function abnormally) before and after they had been treated with medications.

Progress Toward Genomic/Proteomic Therapies

Not only can we identify gene deletions with disease as in the cases of autism and prostate cancer, but also we can manipulate them to control disease, including the disease of aging—at least in common yeast, whose normal one-week lifespan has been extended ten-fold by the deletion of two genes and the imposition of a calorie-restricted diet. Although we are “very, very far from making a person live to 800 years of age,” the scientist responsible for this feat in yeast says, he does think it is possible. Many gerontologists are deeply skeptical of such claims, one calling it “science fiction … also breathtakingly arrogant” and claiming the evidence shows that death at a maximum age of about 125 is inevitable. But the fact that same two genes whose removal led to extreme longevity in yeast also promote aging in humans tends to debunk the old evidence.

Understanding the genetics of disease may be enough for diagnosing it but not always enough for treating it. For that, it helps greatly to understand the proteomic processes initiated by the genes. An imaging technology called coherent two-dimensional infrared spectroscopy (2DIR) has enabled scientists to identify proteins by mapping their internal energy flows. Compared to current methods to identify and count proteins, which use antibodies or mass spectrometry, 2DIR is more sensitive and provides additional information on how protein activity and function is modulated within cells. This could lead to a tool to analyze the protein content of cells, which would be enormously useful for drug discovery, as well as for biomarker discovery and basic biology research.

A proteomic breakthrough in treatment for women who become resistant to breast cancer drugs inhibits the activity of a certain protein in the cancer. The result is that resistance to breast cancer drug tamoxifen is preventable and reversible. AstraZeneca’s experimental drug AZD0530, now in early clinical trials, made tamoxifen-resistant cells sensitive to tamoxifen again, and treating the cells with a combination of tamoxifen and AZD0530 prevented drug resistance from developing in the first place.

Whether we live to 125 or 800, proteomics may at least help reduce the ravages of aging. Proteins are machines, and like all machines are subject to wear and tear. Worn-out or damaged proteins in our cells need to be cleared away and recycled as soon as possible, so they don’t pile up as toxic garbage dumps poisoning the cell. Unfortunately, our cellular waste disposal system becomes progressively less efficient as we age, leading in turn to progressive deterioration in the heart, liver, brain, and other organs.

So researchers created a mouse with two genetic modifications: one to boost the number of cell receptors linked to the protein recycling function; and one to serve as a switch to turn the first one on. The “switch” was activated by modifying the animal’s diet at age six months, when age-related decline in the protein-recycling system begins in mice. By the time the treated mice reached two years of age, their liver cells were found to be much better at recycling protein than those of normal two-year-old mice, and their overall liver function was comparable to much younger mice. The researchers next plan to see, in animal models, if their technique prevents Alzheimer’s and Parkinson’s diseases.

T cells can also be rejuvenated through proteomics. Those in sick mice were reinvigorated by blocking a receptor on the cell surface with an antibody. The method dramatically restored immunity in the mice and could be used in therapies for HIV, hepatitis B and C, cancer, and other diseases. A way was also found to distinguish between T cells that can be revitalized in this way and those that cannot. The research will help in the development of blocking agents, and also in identifying patients likely to benefit most from them. A pharmaceutical company is said to be preparing to test one of these agents in patients with hepatitis C.

Gene Therapy and Tissue Engineering

Our final note on progress toward specific genetic therapies involves freeze-dried tendon implants loaded with gene therapy solution. These implants could accelerate healing and help restore a wide range of movement following injuries to the anterior cruciate ligament, the rotator cuff, and other tissues. Current autograft implants (using tissues taken from elsewhere in the patient) can lead to inflammation and scarring, resulting in friction, pain, and motion disability. Donor graft implants are often rejected by the patient’s immune system, and synthetic scaffolds have failed to match the mechanical strength of human tissue. In mouse tests, the gene-laden implants restored nearly 65 percent of the normal range of motion at 28 days after surgery. In contrast, implants loaded with a non-therapeutic gene restored only 35 percent of the normal range.

Breakthrough for Gene Chips

The conventional gene chips underpinning most of the advances described in this issue are relatively slow to operate and relatively difficult to make. A new platform made from self-assembled DNA nanoarrays called “nanotiles” could analyze gene expression in a single cell, quickly and inexpensively. A single-strand of genomic DNA is programmed to self-assemble as nanotiles containing probes for specific gene expression targets. In a single step, 100 trillion biocompatible and water soluble DNA nanotiles form simultaneously in a solution of a few microliters.

The developers designed three different bar-coded nanotiles to detect three different RNA genes. The different tiles can be mixed together in solution and used for multiplex detection of minute quantities of RNA by an atomic force microscope.

When fully developed (“technical hurdles remain”) the result could revolutionize what is already a revolution in diagnostics. (Incidentally, it might seem oxymoronic to regulate a revolution, but that hasn’t stopped a US government panel from trying. The panel has called for greater regulation of genetic testing as a growing number of consumers buy them. The panel warns that inaccurate test results given by doctors who lack experience with them could cause harm to sick patients in need of correct treatment.) [See the November issue of the Digest for more summaries of articles on genomic regulation.]

The Spliceosome

If number of genes determined how complex an organism would become, we would be less than twice as complex as a fruit fly. What matters is not the number of genes but rather how many different proteins a given set of genes can instruct cells to manufacture. “RNA splicing” is a key part of the process by which this happens, and “alternative splicing” enables even a single gene to order up thousands of different proteins.

Messenger RNA takes an order “spliced” from an activated gene to the ribosome in the cell body, which then makes a protein to order. The protein’s shape, and therefore its function, depends on “splicing factors” that assemble the RNA order in the first place, in a complex called the spliceosome. A team of computational biologists generated predictions about how just two of many splicing factors control regulatory networks involving many other genes, and led them to conclude that “many of the predicted RNA targets play important roles in neuromuscular functions and disorders.”

Clearly there remains a lot to learn beyond the genome, the epigenome, and the proteome, none of which we yet fully understand; but even if we understood all of those plus the spliceosome, we would still not be finished.

Mitochondrial Approach to Cancer Cure

Why? Because we house more than just our own nuclear genome. We also house the genome of our mitochondria, the little aliens that provide the energy to run the proteomic machinery in our cells. Czech and Austrian scientists have found that a vitamin E analog known as VES gave promising results when tested on tumors of the large intestine, lungs, pleura, the mammary gland, and the cervix in mice. The VES targeted a particular spot on mitochondria in cancerous but not in healthy cells, thereby causing the cancer cells to die. They believe their discovery will lead to “very effective” cancer therapy.

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While therapies for the various diseases mentioned in this issue may be some way off, our accelerating understanding of the genetic basis for disease has already resulted in therapies for several other diseases. In the next issue—the last of our three-part series on genomics—we will describe therapies that have already begun to be applied in humans.